Remove "struct detector" completely, part I

record_image has been moved to pattern_sim.c

5 files changed, 127 insertions, 2719 deletions

diff --git a/libcrystfel/CMakeLists.txt b/libcrystfel/CMakeLists.txt
index 32bf6fe3..b3953dbe 100644
--- a/libcrystfel/CMakeLists.txt
+++ b/libcrystfel/CMakeLists.txt
@@ -33,7 +33,6 @@ set(LIBCRYSTFEL_SOURCES
     src/reflist.c
     src/utils.c
     src/cell.c
-    src/detector.c
     src/thread-pool.c
     src/image.c
     src/hdf5-file.c
@@ -83,7 +82,6 @@ set(LIBCRYSTFEL_HEADERS
     src/reflist-utils.h
     src/thread-pool.h
     src/utils.h
-    src/detector.h
     src/geometry.h
     src/peakfinder8.h
     src/peaks.h
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
deleted file mode 100644
index 5653f0f2..00000000
--- a/libcrystfel/src/detector.c
+++ /dev/null
@@ -1,2362 +0,0 @@
-/*
- * detector.c
- *
- * Detector properties
- *
- * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
- *                       a research centre of the Helmholtz Association.
- * Copyright © 2012 Richard Kirian
- *
- * Authors:
- *   2009-2019 Thomas White <taw@physics.org>
- *   2014      Valerio Mariani
- *   2014      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
- *   2011      Andrew Aquila
- *   2011      Richard Kirian <rkirian@asu.edu>
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#include <stdlib.h>
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
-#include <assert.h>
-#include <ctype.h>
-#include <sys/stat.h>
-
-#include "image.h"
-#include "utils.h"
-#include "detector.h"
-#include "hdf5-file.h"
-
-
-/**
- * \file detector.h
- */
-
-
-struct rg_definition {
-	char *name;
-	char *pns;
-};
-
-
-struct rgc_definition {
-	char *name;
-	char *rgs;
-};
-
-
-static int atob(const char *a)
-{
-	if ( strcasecmp(a, "true") == 0 ) return 1;
-	if ( strcasecmp(a, "false") == 0 ) return 0;
-	return atoi(a);
-}
-
-
-static int assplode_algebraic(const char *a_orig, char ***pbits)
-{
-	int len, i;
-	int nexp;
-	char **bits;
-	char *a;
-	int idx, istr;
-
-	len = strlen(a_orig);
-
-	/* Add plus at start if no sign there already */
-	if ( (a_orig[0] != '+') && (a_orig[0] != '-') ) {
-		len += 1;
-		a = malloc(len+1);
-		snprintf(a, len+1, "+%s", a_orig);
-		a[len] = '\0';
-
-	} else {
-		a = strdup(a_orig);
-	}
-
-	/* Count the expressions */
-	nexp = 0;
-	for ( i=0; i<len; i++ ) {
-		if ( (a[i] == '+') || (a[i] == '-') ) nexp++;
-	}
-
-	bits = calloc(nexp, sizeof(char *));
-
-	/* Break the string up */
-	idx = -1;
-	istr = 0;
-	assert((a[0] == '+') || (a[0] == '-'));
-	for ( i=0; i<len; i++ ) {
-
-		char ch;
-
-		ch = a[i];
-
-		if ( (ch == '+') || (ch == '-') ) {
-			if ( idx >= 0 ) bits[idx][istr] = '\0';
-			idx++;
-			bits[idx] = malloc(len+1);
-			istr = 0;
-		}
-
-		if ( !isdigit(ch) && (ch != '.') && (ch != '+') && (ch != '-')
-		  && (ch != 'x') && (ch != 'y') && (ch != 'z') )
-		{
-			ERROR("Invalid character '%c' found.\n", ch);
-			return 0;
-		}
-
-		assert(idx >= 0);
-		bits[idx][istr++] = ch;
-
-	}
-	if ( idx >= 0 ) bits[idx][istr] = '\0';
-
-	*pbits = bits;
-	free(a);
-
-	return nexp;
-}
-
-
-/* Parses the scan directions (accounting for possible rotation)
- * Assumes all white spaces have been already removed */
-static int dir_conv(const char *a, double *sx, double *sy, double *sz)
-{
-	int n;
-	char **bits;
-	int i;
-
-	*sx = 0.0;  *sy = 0.0;  *sz = 0.0;
-
-	n = assplode_algebraic(a, &bits);
-
-	if ( n == 0 ) {
-		ERROR("Invalid direction '%s'\n", a);
-		return 1;
-	}
-
-	for ( i=0; i<n; i++ ) {
-
-		int len;
-		double val;
-		char axis;
-		int j;
-
-		len = strlen(bits[i]);
-		assert(len != 0);
-		axis = bits[i][len-1];
-		if ( (axis != 'x') && (axis != 'y') && (axis != 'z') ) {
-			ERROR("Invalid symbol '%c' - must be x, y or z.\n",
-			      axis);
-			return 1;
-		}
-
-		/* Chop off the symbol now it's dealt with */
-		bits[i][len-1] = '\0';
-
-		/* Check for anything that isn't part of a number */
-		for ( j=0; j<strlen(bits[i]); j++ ) {
-			if ( isdigit(bits[i][j]) ) continue;
-			if ( bits[i][j] == '+' ) continue;
-			if ( bits[i][j] == '-' ) continue;
-			if ( bits[i][j] == '.' ) continue;
-			ERROR("Invalid coefficient '%s'\n", bits[i]);
-		}
-
-		if ( strlen(bits[i]) == 0 ) {
-			val = 1.0;
-		} else {
-			val = atof(bits[i]);
-		}
-		if ( strlen(bits[i]) == 1 ) {
-			if ( bits[i][0] == '+' ) val = 1.0;
-			if ( bits[i][0] == '-' ) val = -1.0;
-		}
-		switch ( axis ) {
-
-			case 'x' :
-			*sx += val;
-			break;
-
-			case 'y' :
-			*sy += val;
-			break;
-
-			case 'z' :
-			*sz += val;
-			break;
-		}
-
-		free(bits[i]);
-
-	}
-	free(bits);
-
-	return 0;
-}
-
-
-static int count_trailing_spaces(const char *string) {
-
-	int i;
-
-	for ( i=0; i<strlen(string); i++ ) {
-		if ( !isspace(string[i]) ) {
-			return i;
-		}
-	}
-
-	return -1;
-}
-
-
-static void build_output_line(const char *line, char *new_line,
-                              const char *string_to_write)
-{
-	int nsp, i, w, ww;
-	int trailsp;
-	int n_bits;
-	char **bits;
-
-	n_bits = assplode(line, "=", &bits, ASSPLODE_NONE);
-	trailsp = count_trailing_spaces(bits[1]);
-
-	strcat(new_line, bits[0]);
-	strcat(new_line, "=");
-
-	for ( nsp=0; nsp < trailsp; nsp++ ) {
-		strcat(new_line, " ");
-	}
-	strcat(new_line, string_to_write);
-
-	for ( w=0; w<strlen(line); w++ ) {
-		if ( strncmp(&line[w],";",1) == 0 ) {
-			for ( ww=w-1; ww>=0; ww-- ) {
-				if ( !isspace(line[ww])) {
-					strcat(new_line, &line[ww]);
-					break;
-				}
-			}
-			break;
-		}
-	}
-	for ( i=0; i<n_bits; i++) free(bits[i]);
-	free(bits);
-}
-
-
-struct rvec get_q_for_panel(struct panel *p, double fs, double ss,
-                            double *ttp, double k)
-{
-	struct rvec q;
-	double ctt, twotheta;
-	double xs, ys, zs;
-	double az;
-
-	/* Calculate 3D position of given position, in m */
-	xs = (p->cnx  + fs*p->fsx + ss*p->ssx) / p->res;
-	ys = (p->cny  + fs*p->fsy + ss*p->ssy) / p->res;
-	zs = p->clen + (fs*p->fsz + ss*p->ssz) / p->res;
-
-	ctt = zs/sqrt(xs*xs + ys*ys + zs*zs);
-	twotheta = acos(ctt);
-	az = atan2(ys, xs);
-	if ( ttp != NULL ) *ttp = twotheta;
-
-	q.u = k * sin(twotheta)*cos(az);
-	q.v = k * sin(twotheta)*sin(az);
-	q.w = k * (ctt - 1.0);
-
-	return q;
-}
-
-
-int in_bad_region(struct detector *det, struct panel *p, double fs, double ss)
-{
-	double rx, ry;
-	double xs, ys;
-	int i;
-
-	/* No panel found -> definitely bad! */
-	if ( p == NULL ) return 1;
-
-	/* Convert xs and ys, which are in fast scan/slow scan coordinates,
-	 * to x and y */
-	xs = fs*p->fsx + ss*p->ssx;
-	ys = fs*p->fsy + ss*p->ssy;
-
-	rx = xs + p->cnx;
-	ry = ys + p->cny;
-
-	for ( i=0; i<det->n_bad; i++ ) {
-
-		struct badregion *b = &det->bad[i];
-
-		if ( (b->panel != NULL)
-		  && (strcmp(b->panel, p->name) != 0) ) continue;
-
-		if ( b->is_fsss ) {
-
-			int nfs, nss;
-
-			/* fs/ss bad regions are specified according to the
-			 * original coordinates */
-			nfs = fs + p->orig_min_fs;
-			nss = ss + p->orig_min_ss;
-
-			if ( nfs < b->min_fs ) continue;
-			if ( nfs > b->max_fs ) continue;
-			if ( nss < b->min_ss ) continue;
-			if ( nss > b->max_ss ) continue;
-
-		} else {
-
-			if ( rx < b->min_x ) continue;
-			if ( rx > b->max_x ) continue;
-			if ( ry < b->min_y ) continue;
-			if ( ry > b->max_y ) continue;
-
-		}
-
-		return 1;
-	}
-
-	return 0;
-}
-
-
-int detector_has_clen_references(struct detector *det)
-{
-	int i;
-
-	for ( i=0; i<det->n_panels; i++ ) {
-		if ( det->panels[i].clen_from != NULL ) return 1;
-	}
-
-	return 0;
-}
-
-
-static void record_panel(struct panel *p, float *dp, int do_poisson,
-                         gsl_rng *rng, double ph_per_e, double background,
-			 double lambda,
-                         int *n_neg1, int *n_inf1, int *n_nan1,
-                         int *n_neg2, int *n_inf2, int *n_nan2,
-			 double *max_tt)
-{
-	int fs, ss;
-
-	for ( ss=0; ss<p->h; ss++ ) {
-	for ( fs=0; fs<p->w; fs++ ) {
-
-		double counts;
-		double cf;
-		double intensity, sa;
-		double pix_area, Lsq;
-		double xs, ys, rx, ry;
-		double dsq, proj_area;
-		float dval;
-		double twotheta;
-
-		intensity = (double)dp[fs + p->w*ss];
-		if ( isinf(intensity) ) (*n_inf1)++;
-		if ( intensity < 0.0 ) (*n_neg1)++;
-		if ( isnan(intensity) ) (*n_nan1)++;
-
-		/* Area of one pixel */
-		pix_area = pow(1.0/p->res, 2.0);
-		Lsq = pow(p->clen, 2.0);
-
-		/* Calculate distance from crystal to pixel */
-		xs = fs*p->fsx + ss*p->ssx;
-		ys = ss*p->fsy + ss*p->ssy;
-		rx = (xs + p->cnx) / p->res;
-		ry = (ys + p->cny) / p->res;
-		dsq = pow(rx, 2.0) + pow(ry, 2.0);
-		twotheta = atan2(sqrt(dsq), p->clen);
-
-		/* Area of pixel as seen from crystal (approximate) */
-		proj_area = pix_area * cos(twotheta);
-
-		/* Projected area of pixel divided by distance squared */
-		sa = proj_area / (dsq + Lsq);
-
-		if ( do_poisson ) {
-			counts = poisson_noise(rng, intensity * ph_per_e * sa);
-		} else {
-			cf = intensity * ph_per_e * sa;
-			counts = cf;
-		}
-
-		/* Number of photons in pixel */
-		dval = counts + poisson_noise(rng, background);
-
-		/* Convert to ADU */
-		dval *= p->adu_per_photon;
-
-		/* Saturation */
-		if ( dval > p->max_adu ) dval = p->max_adu;
-
-		dp[fs + p->w*ss] = dval;
-
-		/* Sanity checks */
-		if ( isinf(dp[fs + p->w*ss]) ) n_inf2++;
-		if ( isnan(dp[fs + p->w*ss]) ) n_nan2++;
-		if ( dp[fs + p->w*ss] < 0.0 ) n_neg2++;
-
-		if ( twotheta > *max_tt ) *max_tt = twotheta;
-
-	}
-	}
-}
-
-
-void record_image(struct image *image, int do_poisson, double background,
-                  gsl_rng *rng, double beam_radius, double nphotons)
-{
-	double total_energy, energy_density;
-	double ph_per_e;
-	double area;
-	double max_tt = 0.0;
-	int n_inf1 = 0;
-	int n_neg1 = 0;
-	int n_nan1 = 0;
-	int n_inf2 = 0;
-	int n_neg2 = 0;
-	int n_nan2 = 0;
-	int pn;
-
-	/* How many photons are scattered per electron? */
-	area = M_PI*pow(beam_radius, 2.0);
-	total_energy = nphotons * ph_lambda_to_en(image->lambda);
-	energy_density = total_energy / area;
-	ph_per_e = (nphotons /area) * pow(THOMSON_LENGTH, 2.0);
-	STATUS("Fluence = %8.2e photons, "
-	       "Energy density = %5.3f kJ/cm^2, "
-	       "Total energy = %5.3f microJ\n",
-	       nphotons, energy_density/1e7, total_energy*1e6);
-
-	fill_in_adu(image);
-
-	for ( pn=0; pn<image->det->n_panels; pn++ ) {
-
-		record_panel(&image->det->panels[pn], image->dp[pn],
-		             do_poisson, rng, ph_per_e, background,
-			     image->lambda,
-		             &n_neg1, &n_inf1, &n_nan1,
-		             &n_neg2, &n_inf2, &n_nan2, &max_tt);
-	}
-
-	STATUS("Max 2theta = %.2f deg, min d = %.2f nm\n",
-	        rad2deg(max_tt), (image->lambda/(2.0*sin(max_tt/2.0)))/1e-9);
-
-	STATUS("Halve the d values to get the voxel size for a synthesis.\n");
-
-	if ( n_neg1 + n_inf1 + n_nan1 + n_neg2 + n_inf2 + n_nan2 ) {
-		ERROR("WARNING: The raw calculation produced %i negative"
-		      " values, %i infinities and %i NaNs.\n",
-		      n_neg1, n_inf1, n_nan1);
-		ERROR("WARNING: After processing, there were %i negative"
-		      " values, %i infinities and %i NaNs.\n",
-		      n_neg2, n_inf2, n_nan2);
-	}
-}
-
-
-signed int find_orig_panel_number(struct detector *det, double fs, double ss)
-{
-	int p;
-
-	for ( p=0; p<det->n_panels; p++ ) {
-		if ( (fs >= det->panels[p].orig_min_fs)
-		  && (fs < det->panels[p].orig_max_fs+1)
-		  && (ss >= det->panels[p].orig_min_ss)
-		  && (ss < det->panels[p].orig_max_ss+1) ) return p;
-	}
-
-	return -1;
-}
-
-
-/* Like find_panel(), but uses the original panel bounds, i.e. referring to
- * what's in the HDF5 file */
-struct panel *find_orig_panel(struct detector *det, double fs, double ss)
-{
-	signed int pn = find_orig_panel_number(det, fs, ss);
-	if ( pn == -1 ) return NULL;
-	return &det->panels[pn];
-}
-
-
-int panel_number(const struct detector *det, const struct panel *p)
-{
-	int pn;
-
-	for ( pn=0; pn<det->n_panels; pn++ ) {
-		if ( &det->panels[pn] == p ) return pn;
-	}
-
-	return det->n_panels;
-}
-
-
-void adjust_centering_for_rail(struct panel *p)
-{
-	double offs;
-
-	/* Offset in +z direction from calibrated clen to actual */
-	offs = p->clen - p->clen_for_centering;
-	p->cnx += p->rail_x * offs;
-	p->cny += p->rail_y * offs;
-	p->clen = p->clen_for_centering + p->coffset + p->rail_z * offs;
-}
-
-
-void fill_in_adu(struct image *image)
-{
-	int i;
-
-	if ( image->det == NULL ) return;
-
-	for ( i=0; i<image->det->n_panels; i++ ) {
-
-		struct panel *p = &image->det->panels[i];
-
-		/* Already have ADU per photon? */
-		if ( !isnan(p->adu_per_photon) ) continue;
-
-		if ( isnan(p->adu_per_eV) ) {
-			ERROR("Neither adu_per_eV nor adu_per_photon set for "
-			      "panel %s\n", p->name);
-			continue;
-		}
-
-		/* Convert ADU per eV to ADU per photon */
-		p->adu_per_photon = ph_lambda_to_eV(image->lambda)
-		                               * p->adu_per_eV;
-	}
-}
-
-
-int panel_is_in_rigid_group(const struct rigid_group *rg, struct panel *p)
-{
-	int i;
-
-	for ( i=0; i<rg->n_panels; i++ ) {
-		if ( rg->panels[i] == p ) {
-			return 1;
-		}
-	}
-
-	return 0;
-}
-
-
-int rigid_group_is_in_collection(struct rg_collection *c,
-                                 struct rigid_group *rg)
-{
-	int i;
-
-	for ( i=0; i<c->n_rigid_groups; i++ ) {
-		if ( c->rigid_groups[i] == rg  ) {
-			return 1;
-		}
-	}
-
-	return 0;
-}
-
-
-struct rg_collection *find_rigid_group_collection_by_name(struct detector *det,
-                                                          const char *name)
-{
-	int i;
-
-	for ( i=0; i<det->n_rg_collections; i++ ) {
-		if ( strcmp(det->rigid_group_collections[i]->name,
-		            name) == 0 ) {
-			return det->rigid_group_collections[i];
-		}
-	}
-
-	return NULL;
-}
-
-
-static struct panel *new_panel(struct detector *det, const char *name)
-{
-	struct panel *new;
-
-	det->n_panels++;
-	det->panels = realloc(det->panels, det->n_panels*sizeof(struct panel));
-
-	new = &det->panels[det->n_panels-1];
-	memcpy(new, &det->defaults, sizeof(struct panel));
-
-	strcpy(new->name, name);
-
-	/* Create a new copy of the camera length location if needed */
-	if ( new->clen_from != NULL ) {
-		new->clen_from = strdup(new->clen_from);
-	}
-
-	/* Create a new copy of the data location if needed */
-	if ( new->data != NULL ) {
-		new->data = strdup(new->data);
-	}
-
-	/* Create a new copy of the dim_structure if needed */
-	if ( new->dim_structure != NULL ) {
-
-		struct dim_structure *dim_copy;
-		int di;
-
-		dim_copy = initialize_dim_structure();
-		dim_copy->num_dims = new->dim_structure->num_dims;
-		dim_copy->dims = malloc(dim_copy->num_dims*sizeof(int));
-		for ( di=0; di<dim_copy->num_dims; di++ ) {
-			dim_copy->dims[di] = new->dim_structure->dims[di];
-		}
-
-		new->dim_structure = dim_copy;
-	}
-
-	/* Create a new copy of the bad pixel mask location */
-	if ( new->mask != NULL ) {
-		new->mask = strdup(new->mask);
-	}
-
-	return new;
-}
-
-
-static struct badregion *new_bad_region(struct detector *det, const char *name)
-{
-	struct badregion *new;
-
-	det->n_bad++;
-	det->bad = realloc(det->bad, det->n_bad*sizeof(struct badregion));
-
-	new = &det->bad[det->n_bad-1];
-	new->min_x = NAN;
-	new->max_x = NAN;
-	new->min_y = NAN;
-	new->max_y = NAN;
-	new->min_fs = 0;
-	new->max_fs = 0;
-	new->min_ss = 0;
-	new->max_ss = 0;
-	new->is_fsss = 99; /* Slightly nasty: means "unassigned" */
-	new->panel = NULL;
-	strcpy(new->name, name);
-
-	return new;
-}
-
-
-struct panel *find_panel_by_name(struct detector *det, const char *name)
-{
-	int i;
-
-	for ( i=0; i<det->n_panels; i++ ) {
-		if ( strcmp(det->panels[i].name, name) == 0 ) {
-			return &det->panels[i];
-		}
-	}
-
-	return NULL;
-}
-
-
-static struct badregion *find_bad_region_by_name(struct detector *det,
-                                                 const char *name)
-{
-	int i;
-
-	for ( i=0; i<det->n_bad; i++ ) {
-		if ( strcmp(det->bad[i].name, name) == 0 ) {
-			return &det->bad[i];
-		}
-	}
-
-	return NULL;
-}
-
-
-static struct rigid_group *find_or_add_rg(struct detector *det,
-                                          const char *name)
-{
-	int i;
-	struct rigid_group **new;
-	struct rigid_group *rg;
-
-	for ( i=0; i<det->n_rigid_groups; i++ ) {
-
-		if ( strcmp(det->rigid_groups[i]->name, name) == 0 ) {
-			return det->rigid_groups[i];
-		}
-
-	}
-
-	new = realloc(det->rigid_groups,
-	              (1+det->n_rigid_groups)*sizeof(struct rigid_group *));
-	if ( new == NULL ) return NULL;
-
-	det->rigid_groups = new;
-
-	rg = malloc(sizeof(struct rigid_group));
-	if ( rg == NULL ) return NULL;
-
-	det->rigid_groups[det->n_rigid_groups++] = rg;
-
-	rg->name = strdup(name);
-	rg->panels = NULL;
-	rg->n_panels = 0;
-
-	return rg;
-}
-
-
-static struct rg_collection *find_or_add_rg_coll(struct detector *det,
-                                                 const char *name)
-{
-	int i;
-	struct rg_collection **new;
-	struct rg_collection *rgc;
-
-	for ( i=0; i<det->n_rg_collections; i++ ) {
-		if ( strcmp(det->rigid_group_collections[i]->name, name) == 0 )
-		{
-			return det->rigid_group_collections[i];
-		}
-	}
-
-	new = realloc(det->rigid_group_collections,
-	              (1+det->n_rg_collections)*sizeof(struct rg_collection *));
-	if ( new == NULL ) return NULL;
-
-	det->rigid_group_collections = new;
-
-	rgc = malloc(sizeof(struct rg_collection));
-	if ( rgc == NULL ) return NULL;
-
-	det->rigid_group_collections[det->n_rg_collections++] = rgc;
-
-	rgc->name = strdup(name);
-	rgc->rigid_groups = NULL;
-	rgc->n_rigid_groups = 0;
-
-	return rgc;
-}
-
-
-static void add_to_rigid_group(struct rigid_group *rg, struct panel *p)
-{
-	struct panel **pn;
-
-	pn = realloc(rg->panels, (1+rg->n_panels)*sizeof(struct panel *));
-	if ( pn == NULL ) {
-		ERROR("Couldn't add panel to rigid group.\n");
-		return;
-	}
-
-	rg->panels = pn;
-	rg->panels[rg->n_panels++] = p;
-}
-
-
-static void add_to_rigid_group_coll(struct rg_collection *rgc,
-                                    struct rigid_group *rg)
-{
-	struct rigid_group **r;
-
-	r = realloc(rgc->rigid_groups, (1+rgc->n_rigid_groups)*
-	            sizeof(struct rigid_group *));
-	if ( r == NULL ) {
-		ERROR("Couldn't add rigid group to collection.\n");
-		return;
-	}
-
-	rgc->rigid_groups = r;
-	rgc->rigid_groups[rgc->n_rigid_groups++] = rg;
-}
-
-
-/* Free all rigid groups in detector */
-static void free_all_rigid_groups(struct detector *det)
-{
-	int i;
-
-	if ( det->rigid_groups == NULL ) return;
-	for ( i=0; i<det->n_rigid_groups; i++ ) {
-		free(det->rigid_groups[i]->name);
-		free(det->rigid_groups[i]->panels);
-		free(det->rigid_groups[i]);
-	}
-	free(det->rigid_groups);
-}
-
-
-/* Free all rigid groups in detector */
-static void free_all_rigid_group_collections(struct detector *det)
-{
-	int i;
-
-	if ( det->rigid_group_collections == NULL ) return;
-	for ( i=0; i<det->n_rg_collections; i++ ) {
-		free(det->rigid_group_collections[i]->name);
-		free(det->rigid_group_collections[i]->rigid_groups);
-		free(det->rigid_group_collections[i]);
-	}
-	free(det->rigid_group_collections);
-}
-
-
-static struct rigid_group *find_rigid_group_by_name(struct detector *det,
-                                                    char *name)
-{
-	int i;
-
-	for ( i=0; i<det->n_rigid_groups; i++ ) {
-		if ( strcmp(det->rigid_groups[i]->name, name) == 0 ) {
-			return det->rigid_groups[i];
-		}
-	}
-
-	return NULL;
-}
-
-
-static int parse_field_for_panel(struct panel *panel, const char *key,
-                                 const char *val, struct detector *det)
-{
-	int reject = 0;
-
-	if ( strcmp(key, "min_fs") == 0 ) {
-		panel->orig_min_fs = atof(val);
-	} else if ( strcmp(key, "max_fs") == 0 ) {
-		panel->orig_max_fs = atof(val);
-	} else if ( strcmp(key, "min_ss") == 0 ) {
-		panel->orig_min_ss = atof(val);
-	} else if ( strcmp(key, "max_ss") == 0 ) {
-		panel->orig_max_ss = atof(val);
-	} else if ( strcmp(key, "corner_x") == 0 ) {
-		panel->cnx = atof(val);
-	} else if ( strcmp(key, "corner_y") == 0 ) {
-		panel->cny = atof(val);
-	} else if ( strcmp(key, "rail_direction") == 0 ) {
-		if ( dir_conv(val, &panel->rail_x,
-		                   &panel->rail_y,
-		                   &panel->rail_z) )
-		{
-			ERROR("Invalid rail direction '%s'\n", val);
-			reject = 1;
-		}
-	} else if ( strcmp(key, "clen_for_centering") == 0 ) {
-		panel->clen_for_centering = atof(val);
-	} else if ( strcmp(key, "adu_per_eV") == 0 ) {
-		panel->adu_per_eV = atof(val);
-	} else if ( strcmp(key, "adu_per_photon") == 0 ) {
-		panel->adu_per_photon = atof(val);
-	} else if ( strcmp(key, "rigid_group") == 0 ) {
-		add_to_rigid_group(find_or_add_rg(det, val), panel);
-	} else if ( strcmp(key, "clen") == 0 ) {
-
-		char *end;
-		double v = strtod(val, &end);
-		if ( end == val ) {
-			/* This means "fill in later" */
-			panel->clen = -1.0;
-			panel->clen_from = strdup(val);
-		} else {
-			panel->clen = v;
-			panel->clen_from = NULL;
-		}
-
-	} else if ( strcmp(key, "data") == 0 ) {
-		if ( strncmp(val,"/",1) != 0 ) {
-			ERROR("Invalid data location '%s'\n", val);
-			reject = -1;
-		}
-		panel->data = strdup(val);
-
-	} else if ( strcmp(key, "mask") == 0 ) {
-		if ( strncmp(val,"/",1) != 0 ) {
-			ERROR("Invalid mask location '%s'\n", val);
-			reject = -1;
-		}
-		panel->mask = strdup(val);
-
-	} else if ( strcmp(key, "mask_file") == 0 ) {
-		panel->mask_file = strdup(val);
-
-	} else if ( strcmp(key, "saturation_map") == 0 ) {
-		panel->satmap = strdup(val);
-	} else if ( strcmp(key, "saturation_map_file") == 0 ) {
-		panel->satmap_file = strdup(val);
-
-	} else if ( strcmp(key, "coffset") == 0) {
-		panel->coffset = atof(val);
-	} else if ( strcmp(key, "res") == 0 ) {
-		panel->res = atof(val);
-	} else if ( strcmp(key, "max_adu") == 0 ) {
-		panel->max_adu = atof(val);
-	} else if ( strcmp(key, "badrow_direction") == 0 ) {
-		panel->badrow = val[0]; /* First character only */
-		if ( (panel->badrow != 'x') && (panel->badrow != 'y')
-		  && (panel->badrow != 'f') && (panel->badrow != 's')
-		  && (panel->badrow != '-') ) {
-			ERROR("badrow_direction must be x, y, f, s or '-'\n");
-			ERROR("Assuming '-'\n.");
-			panel->badrow = '-';
-		}
-		if ( panel->badrow == 'x' ) panel->badrow = 'f';
-		if ( panel->badrow == 'y' ) panel->badrow = 's';
-	} else if ( strcmp(key, "no_index") == 0 ) {
-		panel->no_index = atob(val);
-	} else if ( strcmp(key, "fs") == 0 ) {
-		if ( dir_conv(val, &panel->fsx, &panel->fsy, &panel->fsz) != 0 )
-		{
-			ERROR("Invalid fast scan direction '%s'\n", val);
-			reject = 1;
-		}
-	} else if ( strcmp(key, "ss") == 0 ) {
-		if ( dir_conv(val, &panel->ssx, &panel->ssy, &panel->ssz) != 0 )
-		{
-			ERROR("Invalid slow scan direction '%s'\n", val);
-			reject = 1;
-		}
-	} else if ( strncmp(key, "dim", 3) == 0) {
-		int dim_entry;
-		char *endptr;
-		if ( key[3] != '\0' ) {
-			if  ( panel->dim_structure == NULL ) {
-				panel->dim_structure = initialize_dim_structure();
-			}
-			dim_entry = strtoul(key+3, &endptr, 10);
-			if ( endptr[0] != '\0' ) {
-				ERROR("Invalid dimension number %s\n", key+3);
-			} else {
-				if ( set_dim_structure_entry(panel->dim_structure,
-				                        dim_entry, val) )
-				{
-					ERROR("Failed to set dim structure entry\n");
-				}
-			}
-		} else {
-			ERROR("'dim' must be followed by a number, e.g. 'dim0'\n");
-		}
-	} else {
-		ERROR("Unrecognised field '%s'\n", key);
-	}
-
-	return reject;
-}
-
-
-static int check_badr_fsss(struct badregion *badr, int is_fsss)
-{
-	/* First assignment? */
-	if ( badr->is_fsss == 99 ) {
-		badr->is_fsss = is_fsss;
-		return 0;
-	}
-
-	if ( is_fsss != badr->is_fsss ) {
-		ERROR("You can't mix x/y and fs/ss in a bad region.\n");
-		return 1;
-	}
-
-	return 0;
-}
-
-
-static int parse_field_bad(struct badregion *badr, const char *key,
-                           const char *val)
-{
-	int reject = 0;
-
-	if ( strcmp(key, "min_x") == 0 ) {
-		badr->min_x = atof(val);
-		reject = check_badr_fsss(badr, 0);
-	} else if ( strcmp(key, "max_x") == 0 ) {
-		badr->max_x = atof(val);
-		reject = check_badr_fsss(badr, 0);
-	} else if ( strcmp(key, "min_y") == 0 ) {
-		badr->min_y = atof(val);
-		reject = check_badr_fsss(badr, 0);
-	} else if ( strcmp(key, "max_y") == 0 ) {
-		badr->max_y = atof(val);
-		reject = check_badr_fsss(badr, 0);
-	} else if ( strcmp(key, "min_fs") == 0 ) {
-		badr->min_fs = atof(val);
-		reject = check_badr_fsss(badr, 1);
-	} else if ( strcmp(key, "max_fs") == 0 ) {
-		badr->max_fs = atof(val);
-		reject = check_badr_fsss(badr, 1);
-	} else if ( strcmp(key, "min_ss") == 0 ) {
-		badr->min_ss = atof(val);
-		reject = check_badr_fsss(badr, 1);
-	} else if ( strcmp(key, "max_ss") == 0 ) {
-		badr->max_ss = atof(val);
-		reject = check_badr_fsss(badr, 1);
-	} else if ( strcmp(key, "panel") == 0 ) {
-		badr->panel = strdup(val);
-	} else {
-		ERROR("Unrecognised field '%s'\n", key);
-	}
-
-	return reject;
-}
-
-
-static void parse_toplevel(struct detector *det, struct beam_params *beam,
-                           const char *key, const char *val,
-                           struct rg_definition ***rg_defl,
-                           struct rgc_definition ***rgc_defl, int *n_rg_defs,
-                           int *n_rgc_defs, char **hdf5_peak_path)
-{
-
-	if ( strcmp(key, "mask_bad") == 0 ) {
-
-		char *end;
-		double v = strtod(val, &end);
-
-		if ( end != val ) {
-			det->mask_bad = v;
-		}
-
-	} else if ( strcmp(key, "mask_good") == 0 ) {
-
-		char *end;
-		double v = strtod(val, &end);
-
-		if ( end != val ) {
-			det->mask_good = v;
-		}
-
-	} else if ( strcmp(key, "coffset") == 0 ) {
-		det->defaults.coffset = atof(val);
-
-	} else if ( strcmp(key, "photon_energy") == 0 ) {
-		if ( beam != NULL ) {
-			double v;
-			char *end;
-			v = strtod(val, &end);
-			if ( (val[0] != '\0') && (end[0] == '\0') ) {
-				beam->photon_energy = v;
-				beam->photon_energy_from = NULL;
-			} else {
-				beam->photon_energy = 0.0;
-				beam->photon_energy_from = strdup(val);
-			}
-		}
-
-	} else if ( strcmp(key, "photon_energy_bandwidth") == 0 ) {
-		if ( beam != NULL ) {
-			double v;
-			char *end;
-			v = strtod(val, &end);
-			if ( (val[0] != '\0') && (end[0] == '\0') ) {
-				beam->bandwidth = v;
-			} else {
-				ERROR("Invalid value for "
-				      "photon_energy_bandwidth\n");
-			}
-		}
-
-	} else if ( strcmp(key, "photon_energy_scale") == 0 ) {
-		if ( beam != NULL ) {
-			beam->photon_energy_scale = atof(val);
-		}
-
-	} else if ( strcmp(key, "peak_info_location") == 0 ) {
-		if ( hdf5_peak_path != NULL ) {
-			*hdf5_peak_path = strdup(val);
-		}
-
-	} else if (strncmp(key, "rigid_group", 11) == 0
-	        && strncmp(key, "rigid_group_collection", 22) != 0 ) {
-
-		struct rg_definition **new;
-
-		new = realloc(*rg_defl,
-		             ((*n_rg_defs)+1)*sizeof(struct rg_definition*));
-		*rg_defl = new;
-
-		(*rg_defl)[*n_rg_defs] = malloc(sizeof(struct rg_definition));
-		(*rg_defl)[*n_rg_defs]->name = strdup(key+12);
-		(*rg_defl)[*n_rg_defs]->pns = strdup(val);
-		*n_rg_defs = *n_rg_defs+1;
-
-	} else if ( strncmp(key, "rigid_group_collection", 22) == 0 ) {
-
-		struct rgc_definition **new;
-
-		new = realloc(*rgc_defl, ((*n_rgc_defs)+1)*
-		      sizeof(struct rgc_definition*));
-		*rgc_defl = new;
-
-		(*rgc_defl)[*n_rgc_defs] =
-		                   malloc(sizeof(struct rgc_definition));
-		(*rgc_defl)[*n_rgc_defs]->name = strdup(key+23);
-		(*rgc_defl)[*n_rgc_defs]->rgs = strdup(val);
-		*n_rgc_defs = *n_rgc_defs+1;
-
-	} else if ( parse_field_for_panel(&det->defaults, key, val, det) ) {
-		ERROR("Unrecognised top level field '%s'\n", key);
-	}
-}
-
-
-/* Test if fs,ss in panel "p" is further {out,in} than {*p_max_d,*p_min_d}, and
- * if so update det->furthest_{out,in}_{panel,fs,ss}. */
-static void check_point(struct panel *p, double fs, double ss,
-                        double *p_min_d, double *p_max_d, struct detector *det)
-{
-	double xs, ys, rx, ry, d;
-
-	xs = fs*p->fsx + ss*p->ssx;
-	ys = fs*p->fsy + ss*p->ssy;
-
-	rx = (xs + p->cnx) / p->res;
-	ry = (ys + p->cny) / p->res;
-
-	d = sqrt(pow(rx, 2.0) + pow(ry, 2.0));
-
-	if ( d > *p_max_d ) {
-
-		det->furthest_out_panel = p;
-		det->furthest_out_fs = fs;
-		det->furthest_out_ss = ss;
-		*p_max_d = d;
-
-	} else if ( d < *p_min_d ) {
-
-		det->furthest_in_panel = p;
-		det->furthest_in_fs = fs;
-		det->furthest_in_ss = ss;
-		*p_min_d = d;
-
-	}
-}
-
-
-static void find_min_max_d(struct detector *det)
-{
-	double max_d, min_d;
-	int i;
-
-	min_d = +INFINITY;
-	max_d = 0.0;
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		struct panel *p;
-
-		p = &det->panels[i];
-
-		check_point(p, 0,    0, &min_d, &max_d, det);
-		check_point(p, p->w, 0, &min_d, &max_d, det);
-		check_point(p, 0,    p->h, &min_d, &max_d, det);
-		check_point(p, p->w, p->h, &min_d, &max_d, det);
-
-	}
-}
-
-
-struct detector *get_detector_geometry(const char *filename,
-                                       struct beam_params *beam)
-{
-	return get_detector_geometry_2(filename, beam, NULL);
-}
-
-
-struct detector *get_detector_geometry_from_string(const char *string_in,
-                                                   struct beam_params *beam,
-                                                   char **hdf5_peak_path)
-{
-	struct detector *det;
-	char **bits;
-	int done = 0;
-	int i;
-	int rgi, rgci;
-	int reject = 0;
-	int path_dim, mask_path_dim;
-	int dim_dim;
-	int dim_reject = 0;
-	int dim_dim_reject = 0;
-	struct rg_definition **rg_defl = NULL;
-	struct rgc_definition **rgc_defl = NULL;
-	int n_rg_definitions = 0;
-	int n_rgc_definitions = 0;
-	char *string;
-	char *string_orig;
-	size_t len;
-
-	det = calloc(1, sizeof(struct detector));
-	if ( det == NULL ) return NULL;
-
-	if ( beam != NULL ) {
-		beam->photon_energy = 0.0;
-		beam->photon_energy_from = NULL;
-		beam->photon_energy_scale = 1.0;
-		beam->bandwidth = 0.00000001;
-	}
-
-	det->n_panels = 0;
-	det->panels = NULL;
-	det->n_bad = 0;
-	det->bad = NULL;
-	det->mask_good = 0;
-	det->mask_bad = 0;
-	det->n_rigid_groups = 0;
-	det->rigid_groups = NULL;
-	det->path_dim = 0;
-	det->dim_dim = 0;
-	det->n_rg_collections = 0;
-	det->rigid_group_collections = NULL;
-
-	/* The default defaults... */
-	det->defaults.orig_min_fs = -1;
-	det->defaults.orig_min_ss = -1;
-	det->defaults.orig_max_fs = -1;
-	det->defaults.orig_max_ss = -1;
-	det->defaults.cnx = NAN;
-	det->defaults.cny = NAN;
-	det->defaults.clen = NAN;
-	det->defaults.coffset = 0.0;
-	det->defaults.res = -1.0;
-	det->defaults.badrow = '-';
-	det->defaults.no_index = 0;
-	det->defaults.fsx = 1.0;
-	det->defaults.fsy = 0.0;
-	det->defaults.fsz = 0.0;
-	det->defaults.ssx = 0.0;
-	det->defaults.ssy = 1.0;
-	det->defaults.ssz = 0.0;
-        det->defaults.rail_x = NAN;  /* The actual default rail direction */
-        det->defaults.rail_y = NAN;  /*  is below */
-        det->defaults.rail_z = NAN;
-        det->defaults.clen_for_centering = NAN;
-	det->defaults.adu_per_eV = NAN;
-	det->defaults.adu_per_photon = NAN;
-	det->defaults.max_adu = +INFINITY;
-	det->defaults.mask = NULL;
-	det->defaults.mask_file = NULL;
-	det->defaults.satmap = NULL;
-	det->defaults.satmap_file = NULL;
-	det->defaults.data = NULL;
-	det->defaults.dim_structure = NULL;
-	strncpy(det->defaults.name, "", 1023);
-
-	string = strdup(string_in);
-	if ( string == NULL ) return NULL;
-	len = strlen(string);
-	for ( i=0; i<len; i++ ) {
-		if ( string_in[i] == '\r' ) string[i] = '\n';
-	}
-
-	/* Because 'string' will get modified */
-	string_orig = string;
-
-	do {
-
-		int n1, n2;
-		char **path;
-		char *line;
-		struct badregion *badregion = NULL;
-		struct panel *panel = NULL;
-		char wholeval[1024];
-
-		const char *nl = strchr(string, '\n');
-		if ( nl != NULL ) {
-			size_t len = nl - string;
-			line = strndup(string, nl-string);
-			line[len] = '\0';
-			string += len+1;
-		} else {
-			line = strdup(string);
-			done = 1;
-		}
-
-		if ( line[0] == ';' ) {
-			free(line);
-			continue;
-		}
-
-		n1 = assplode(line, " \t", &bits, ASSPLODE_NONE);
-		if ( n1 < 3 ) {
-			for ( i=0; i<n1; i++ ) free(bits[i]);
-			free(bits);
-			free(line);
-			continue;
-		}
-
-		/* Stitch the pieces of the "value" back together */
-		wholeval[0] = '\0';  /* Empty string */
-		for ( i=2; i<n1; i++ ) {
-			if ( bits[i][0] == ';' ) break;  /* Stop on comment */
-			strncat(wholeval, bits[i], 1023);
-		}
-
-		if ( bits[1][0] != '=' ) {
-			for ( i=0; i<n1; i++ ) free(bits[i]);
-			free(bits);
-			free(line);
-			continue;
-		}
-
-		n2 = assplode(bits[0], "/\\.", &path, ASSPLODE_NONE);
-		if ( n2 < 2 ) {
-
-			/* This was a top-level option, not handled above. */
-			parse_toplevel(det, beam, bits[0], wholeval, &rg_defl,
-			               &rgc_defl, &n_rg_definitions,
-				       &n_rgc_definitions, hdf5_peak_path);
-			for ( i=0; i<n1; i++ ) free(bits[i]);
-			free(bits);
-			for ( i=0; i<n2; i++ ) free(path[i]);
-			free(path);
-			free(line);
-			continue;
-		}
-
-		if ( strncmp(path[0], "bad", 3) == 0 ) {
-			badregion = find_bad_region_by_name(det, path[0]);
-			if ( badregion == NULL ) {
-				badregion = new_bad_region(det, path[0]);
-			}
-		} else {
-			panel = find_panel_by_name(det, path[0]);
-			if ( panel == NULL ) {
-				panel = new_panel(det, path[0]);
-			}
-		}
-
-		if ( panel != NULL ) {
-			if ( parse_field_for_panel(panel, path[1],
-			                           wholeval, det) )
-			{
-				reject = 1;
-			}
-		} else {
-			if ( parse_field_bad(badregion, path[1], wholeval) ) {
-				reject = 1;
-			}
-		}
-
-		for ( i=0; i<n1; i++ ) free(bits[i]);
-		for ( i=0; i<n2; i++ ) free(path[i]);
-		free(bits);
-		free(path);
-		free(line);
-
-	} while ( !done );
-
-	if ( det->n_panels == -1 ) {
-		ERROR("No panel descriptions in geometry file.\n");
-		free(det);
-		return NULL;
-	}
-
-	path_dim = -1;
-	dim_reject = 0;
-
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		int panel_dim = 0;
-		char *next_instance;
-
-		next_instance = det->panels[i].data;
-
-		while ( next_instance ) {
-			next_instance = strstr(next_instance, "%");
-			if ( next_instance != NULL ) {
-				next_instance += 1*sizeof(char);
-				panel_dim += 1;
-			}
-		}
-
-		if ( path_dim == -1 ) {
-			path_dim = panel_dim;
-		} else {
-			if ( panel_dim != path_dim ) {
-				dim_reject = 1;
-			}
-		}
-
-	}
-
-	mask_path_dim = -1;
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		int panel_mask_dim = 0;
-		char *next_instance;
-
-		if ( det->panels[i].mask != NULL ) {
-
-			next_instance = det->panels[i].mask;
-
-			while ( next_instance ) {
-				next_instance = strstr(next_instance, "%");
-				if ( next_instance != NULL ) {
-					next_instance += 1*sizeof(char);
-					panel_mask_dim += 1;
-				}
-			}
-
-			if ( mask_path_dim == -1 ) {
-				mask_path_dim = panel_mask_dim;
-			} else {
-				if ( panel_mask_dim != mask_path_dim ) {
-					dim_reject = 1;
-				}
-			}
-
-		}
-	}
-
-	if ( dim_reject ==  1 ) {
-		ERROR("All panels' data and mask entries must have the same "
-		      "number of placeholders\n");
-		reject = 1;
-	}
-
-	if ( mask_path_dim > path_dim ) {
-		ERROR("Number of placeholders in mask cannot be larger than "
-		      "for data\n");
-		reject = 1;
-	}
-
-	det->path_dim = path_dim;
-
-	dim_dim_reject = 0;
-	dim_dim = -1;
-
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		int di;
-		int found_ss = 0;
-		int found_fs = 0;
-		int panel_dim_dim = 0;
-
-		if ( det->panels[i].dim_structure == NULL ) {
-			det->panels[i].dim_structure = default_dim_structure();
-		}
-
-		for ( di=0; di<det->panels[i].dim_structure->num_dims; di++ ) {
-
-			if ( det->panels[i].dim_structure->dims[di] ==
-			                                   HYSL_UNDEFINED  ) {
-				dim_dim_reject = 1;
-				ERROR("Dimension %i for panel %s is undefined.\n",
-				      di, det->panels[i].name);
-			}
-			if ( det->panels[i].dim_structure->dims[di] ==
-			                                   HYSL_PLACEHOLDER  ) {
-				panel_dim_dim += 1;
-			}
-			if ( det->panels[i].dim_structure->dims[di] ==
-			                                   HYSL_SS  ) {
-				found_ss += 1;
-			}
-			if ( det->panels[i].dim_structure->dims[di] ==
-			                                   HYSL_FS  ) {
-				found_fs += 1;
-			}
-
-		}
-
-		if ( found_ss != 1 ) {
-			ERROR("Exactly one slow scan dim coordinate is needed "
-			      "(found %i for panel %s)\n", found_ss,
-			      det->panels[i].name);
-			dim_dim_reject = 1;
-		}
-
-		if ( found_fs != 1 ) {
-			ERROR("Exactly one fast scan dim coordinate is needed "
-			      "(found %i for panel %s)\n", found_fs,
-			      det->panels[i].name);
-			dim_dim_reject = 1;
-		}
-
-		if ( panel_dim_dim > 1 ) {
-			ERROR("Maximum one placeholder dim coordinate is "
-			      "allowed (found %i for panel %s)\n",
-			      panel_dim_dim, det->panels[i].name);
-			dim_dim_reject = 1;
-		}
-
-		if ( dim_dim == -1 ) {
-			dim_dim = panel_dim_dim;
-		} else {
-			if ( panel_dim_dim != dim_dim ) {
-				dim_dim_reject = 1;
-			}
-		}
-
-	}
-
-	if ( dim_dim_reject ==  1) {
-		reject = 1;
-	}
-
-	det->dim_dim = dim_dim;
-
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		struct panel *p = &det->panels[i];
-
-		if ( p->orig_min_fs < 0 ) {
-			ERROR("Please specify the minimum FS coordinate for"
-			      " panel %s\n", det->panels[i].name);
-			reject = 1;
-		}
-		if ( p->orig_max_fs < 0 ) {
-			ERROR("Please specify the maximum FS coordinate for"
-			      " panel %s\n", det->panels[i].name);
-			reject = 1;
-		}
-		if ( p->orig_min_ss < 0 ) {
-			ERROR("Please specify the minimum SS coordinate for"
-			      " panel %s\n", det->panels[i].name);
-			reject = 1;
-		}
-		if ( p->orig_max_ss < 0 ) {
-			ERROR("Please specify the maximum SS coordinate for"
-			      " panel %s\n", det->panels[i].name);
-			reject = 1;
-		}
-		if ( isnan(p->cnx) ) {
-			ERROR("Please specify the corner X coordinate for"
-			      " panel %s\n", det->panels[i].name);
-			reject = 1;
-		}
-		if ( isnan(p->cny) ) {
-			ERROR("Please specify the corner Y coordinate for"
-			      " panel %s\n", det->panels[i].name);
-			reject = 1;
-		}
-		if ( isnan(p->clen) && (p->clen_from == NULL) ) {
-			ERROR("Please specify the camera length for"
-			      " panel %s\n", det->panels[i].name);
-			reject = 1;
-		}
-		if ( p->res < 0 ) {
-			ERROR("Please specify the resolution for"
-			      " panel %s\n", det->panels[i].name);
-			reject = 1;
-		}
-		if ( isnan(p->adu_per_eV) && isnan(p->adu_per_photon) ) {
-			ERROR("Please specify either adu_per_eV or "
-			      "adu_per_photon for panel %s\n",
-			      det->panels[i].name);
-			reject = 1;
-		}
-
-		if ( isnan(p->clen_for_centering) && !isnan(p->rail_x) )
-		{
-			ERROR("You must specify clen_for_centering if you "
-			      "specify the rail direction (panel %s)\n",
-			      p->name);
-			reject = 1;
-		}
-
-		if ( (p->mask_file != NULL) && (p->mask == NULL) ) {
-			ERROR("You have specified 'mask_file' but not 'mask'.  "
-			      "'mask_file' will therefore have no effect.  "
-			      "(panel %s)\n", p->name);
-			reject = 1;
-		}
-
-		/* The default rail direction */
-		if ( isnan(p->rail_x) ) {
-			p->rail_x = 0.0;
-			p->rail_y = 0.0;
-			p->rail_z = 1.0;
-		}
-		if ( isnan(p->clen_for_centering) ) p->clen_for_centering = 0.0;
-
-		/* It's OK if the badrow direction is '0' */
-		/* It's not a problem if "no_index" is still zero */
-		/* The default transformation matrix is at least valid */
-
-		det->panels[i].w = det->panels[i].orig_max_fs
-		                 - det->panels[i].orig_min_fs+1;
-		det->panels[i].h = det->panels[i].orig_max_ss
-		                 - det->panels[i].orig_min_ss+1;
-
-	}
-
-	for ( i=0; i<det->n_bad; i++ ) {
-		if ( det->bad[i].is_fsss == 99 ) {
-			ERROR("Please specify the coordinate ranges for"
-			      " bad region %s\n", det->bad[i].name);
-			reject = 1;
-		}
-	}
-
-	free(det->defaults.clen_from);
-	free(det->defaults.data);
-	free(det->defaults.mask);
-
-	for ( rgi=0; rgi<n_rg_definitions; rgi++) {
-
-		int pi, n1;
-		struct rigid_group *rigidgroup = NULL;
-
-		rigidgroup = find_or_add_rg(det, rg_defl[rgi]->name);
-
-		n1 = assplode(rg_defl[rgi]->pns, ",", &bits, ASSPLODE_NONE);
-
-		for ( pi=0; pi<n1; pi++ ) {
-
-			struct panel *p;
-
-			p = find_panel_by_name(det, bits[pi]);
-			if ( p == NULL ) {
-				ERROR("Cannot add panel to rigid group\n");
-				ERROR("Panel not found: %s\n", bits[pi]);
-				return NULL;
-			}
-			add_to_rigid_group(rigidgroup, p);
-			free(bits[pi]);
-		}
-		free(bits);
-		free(rg_defl[rgi]->name);
-		free(rg_defl[rgi]->pns);
-		free(rg_defl[rgi]);
-	}
-	free(rg_defl);
-
-	for ( rgci=0; rgci<n_rgc_definitions; rgci++ ) {
-
-		int rgi, n2;
-		struct rg_collection *rgcollection = NULL;
-
-		rgcollection = find_or_add_rg_coll(det, rgc_defl[rgci]->name);
-
-		n2 = assplode(rgc_defl[rgci]->rgs, ",", &bits, ASSPLODE_NONE);
-
-		for ( rgi=0; rgi<n2; rgi++ ) {
-
-			struct rigid_group *r;
-
-			r = find_rigid_group_by_name(det, bits[rgi]);
-			if ( r == NULL ) {
-				ERROR("Cannot add rigid group to collection\n");
-				ERROR("Rigid group not found: %s\n", bits[rgi]);
-				return NULL;
-			}
-			add_to_rigid_group_coll(rgcollection, r);
-			free(bits[rgi]);
-		}
-		free(bits);
-		free(rgc_defl[rgci]->name);
-		free(rgc_defl[rgci]->rgs);
-		free(rgc_defl[rgci]);
-
-	}
-	free(rgc_defl);
-
-	if ( n_rg_definitions == 0 ) {
-
-		int pi;
-
-		for ( pi=0; pi<det->n_panels; pi++ ) {
-
-			struct rigid_group *rigidgroup = NULL;
-
-			rigidgroup = find_or_add_rg(det, det->panels[pi].name);
-			add_to_rigid_group(rigidgroup, &det->panels[pi]);
-
-		}
-	}
-
-	if ( n_rgc_definitions == 0 ) {
-
-		int rgi;
-		struct rg_collection *rgcollection = NULL;
-
-		rgcollection = find_or_add_rg_coll(det, "default");
-
-		for ( rgi=0; rgi<det->n_rigid_groups; rgi++ ) {
-
-			add_to_rigid_group_coll(rgcollection,
-			                        det->rigid_groups[rgi]);
-
-		}
-	}
-
-	/* Calculate matrix inverses and other stuff */
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		struct panel *p;
-		double d;
-
-		p = &det->panels[i];
-
-		if ( p->fsx*p->ssy == p->ssx*p->fsy ) {
-			ERROR("Panel %i transformation singular.\n", i);
-		}
-
-		d = (double)p->fsx*p->ssy - p->ssx*p->fsy;
-		p->xfs = p->ssy / d;
-		p->yfs = -p->ssx / d;
-		p->xss = -p->fsy / d;
-		p->yss = p->fsx / d;
-
-		p->w = p->orig_max_fs - p->orig_min_fs + 1;
-		p->h = p->orig_max_ss - p->orig_min_ss + 1;
-
-	}
-
-	find_min_max_d(det);
-	free(string_orig);
-
-	if ( reject ) return NULL;
-
-	return det;
-}
-
-
-struct detector *get_detector_geometry_2(const char *filename,
-                                         struct beam_params *beam,
-                                         char **hdf5_peak_path)
-{
-	char *contents;
-	struct detector *det;
-
-	contents = load_entire_file(filename);
-	if ( contents == NULL ) {
-		ERROR("Failed to load geometry file '%s'\n", filename);
-		return NULL;
-	}
-
-	det = get_detector_geometry_from_string(contents, beam, hdf5_peak_path);
-	free(contents);
-	return det;
-}
-
-
-void free_detector_geometry(struct detector *det)
-{
-	int i;
-
-	free_all_rigid_groups(det);
-	free_all_rigid_group_collections(det);
-
-	for ( i=0; i<det->n_panels; i++ ) {
-		free(det->panels[i].clen_from);
-		free_dim_structure(det->panels[i].dim_structure);
-	}
-
-	free(det->panels);
-	free(det->bad);
-	free(det);
-}
-
-
-static int rg_number(const struct detector *det, const struct rigid_group *rg)
-{
-	int i;
-	for ( i=0; i<det->n_rigid_groups; i++ ) {
-		if ( det->rigid_groups[i] == rg ) return i;
-	}
-	return det->n_rigid_groups;
-}
-
-
-struct detector *copy_geom(const struct detector *in)
-{
-	struct detector *out;
-	int i;
-
-	if ( in == NULL ) return NULL;
-
-	out = malloc(sizeof(struct detector));
-	if ( out == NULL ) return NULL;
-
-	/* Copy everything */
-	memcpy(out, in, sizeof(struct detector));
-
-	out->panels = malloc(out->n_panels * sizeof(struct panel));
-	memcpy(out->panels, in->panels, out->n_panels * sizeof(struct panel));
-
-	out->bad = malloc(out->n_bad * sizeof(struct badregion));
-	memcpy(out->bad, in->bad, out->n_bad * sizeof(struct badregion));
-
-	/* Copy the panels */
-	for ( i=0; i<out->n_panels; i++ ) {
-
-		struct panel *p;
-
-		/* Copy all fields */
-		p = &out->panels[i];
-
-		/* Now fix up everything involving pointers... */
-
-		if ( p->clen_from != NULL ) {
-			/* Make a copy of the clen_from fields unique to this
-			 * copy of the structure. */
-			p->clen_from = strdup(p->clen_from);
-		}
-
-		if ( p->data != NULL ) {
-			/* Make a copy of the data fields unique to this
-			 * copy of the structure. */
-			p->data = strdup(p->data);
-		}
-
-		if ( p->dim_structure != NULL ) {
-			/* Make a copy of the dim_structure fields unique to this
-			 * copy of the structure. */
-
-			struct dim_structure *dim_new;
-			int di;
-
-			dim_new = initialize_dim_structure();
-			dim_new->num_dims = p->dim_structure->num_dims;
-			dim_new->dims = malloc(dim_new->num_dims*sizeof(int));
-			for ( di=0; di<dim_new->num_dims; di++ ) {
-				dim_new->dims[di] = p->dim_structure->dims[di];
-			}
-
-			p->dim_structure = dim_new;
-
-		}
-
-		if ( &in->panels[i] == in->furthest_out_panel ) {
-			out->furthest_out_panel = &out->panels[i];
-		}
-		if ( &in->panels[i] == in->furthest_in_panel ) {
-			out->furthest_in_panel = &out->panels[i];
-		}
-
-	}
-
-	/* Copy all the rigid groups */
-	out->rigid_groups = malloc(out->n_rigid_groups*sizeof(struct rigid_group));
-	if ( out->rigid_groups == NULL ) return NULL;
-	for ( i=0; i<out->n_rigid_groups; i++ ) {
-
-		struct rigid_group *inrg;
-		struct rigid_group *rg;
-		int j;
-
-		rg = malloc(sizeof(struct rigid_group));
-		if ( rg == NULL ) return NULL;
-
-		out->rigid_groups[i] = rg;
-
-		inrg = in->rigid_groups[i];
-
-		rg->name = strdup(inrg->name);
-		if ( rg->name == NULL ) return NULL;
-
-		rg->n_panels = inrg->n_panels;
-		rg->panels = malloc(inrg->n_panels*sizeof(struct panel *));
-		if ( rg->panels == NULL ) return NULL;
-
-		for ( j=0; j<rg->n_panels; j++ ) {
-			int k = panel_number(in, inrg->panels[j]);
-			rg->panels[j] = &out->panels[k];
-		}
-
-	}
-
-	/* Copy all the rigid group collections */
-	out->rigid_group_collections = malloc(out->n_rg_collections*sizeof(struct rg_collection));
-	if ( out->rigid_group_collections == NULL ) return NULL;
-	for ( i=0; i<out->n_rg_collections; i++ ) {
-
-		struct rg_collection *inrgc;
-		struct rg_collection *rgc;
-		int j;
-
-		rgc = malloc(sizeof(struct rg_collection));
-		if ( rgc == NULL ) return NULL;
-
-		out->rigid_group_collections[i] = rgc;
-
-		inrgc = in->rigid_group_collections[i];
-
-		rgc->name = strdup(inrgc->name);
-		if ( rgc->name == NULL ) return NULL;
-
-		rgc->n_rigid_groups = inrgc->n_rigid_groups;
-		rgc->rigid_groups = malloc(rgc->n_rigid_groups*sizeof(struct rg_collection));
-		if ( rgc->rigid_groups == NULL ) return NULL;
-
-		for ( j=0; j<rgc->n_rigid_groups; j++ ) {
-			int k = rg_number(in, inrgc->rigid_groups[j]);
-			if ( k == in->n_rigid_groups ) return NULL;
-			rgc->rigid_groups[j] = out->rigid_groups[k];
-		}
-
-	}
-
-	return out;
-}
-
-
-struct detector *simple_geometry(const struct image *image, int w, int h)
-{
-	struct detector *geom;
-
-	geom = calloc(1, sizeof(struct detector));
-
-	geom->n_panels = 1;
-	geom->panels = calloc(1, sizeof(struct panel));
-
-	geom->panels[0].orig_min_fs = 0;
-	geom->panels[0].orig_max_fs = w-1;
-	geom->panels[0].orig_min_ss = 0;
-	geom->panels[0].orig_max_ss = h-1;
-	geom->panels[0].cnx = -w / 2.0;
-	geom->panels[0].cny = -h / 2.0;
-	geom->panels[0].max_adu = INFINITY;
-	geom->panels[0].orig_min_fs = -1;
-	geom->panels[0].orig_max_fs = -1;
-	geom->panels[0].orig_min_ss = -1;
-	geom->panels[0].orig_max_ss = -1;
-
-	geom->panels[0].fsx = 1;
-	geom->panels[0].fsy = 0;
-	geom->panels[0].fsz = 0;
-	geom->panels[0].ssx = 0;
-	geom->panels[0].ssy = 1;
-	geom->panels[0].ssz = 0;
-
-	geom->panels[0].xfs = 1;
-	geom->panels[0].xss = 0;
-	geom->panels[0].yfs = 0;
-	geom->panels[0].yss = 1;
-
-	geom->panels[0].w = w;
-	geom->panels[0].h = h;
-
-	geom->panels[0].mask = NULL;
-	geom->panels[0].data = NULL;
-
-	find_min_max_d(geom);
-
-	return geom;
-}
-
-
-int reverse_2d_mapping(double x, double y, struct detector *det,
-                       struct panel **pp, double *pfs, double *pss)
-{
-	int i;
-
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		struct panel *p = &det->panels[i];
-		double cx, cy, fs, ss;
-
-		/* Get position relative to corner */
-		cx = x - p->cnx;
-		cy = y - p->cny;
-
-		/* Reverse the transformation matrix */
-		fs = cx*p->xfs + cy*p->yfs;
-		ss = cx*p->xss + cy*p->yss;
-
-		/* In range? */
-		if ( fs < 0 ) continue;
-		if ( ss < 0 ) continue;
-		if ( fs > p->w ) continue;
-		if ( ss > p->h ) continue;
-
-		*pfs = fs;
-		*pss = ss;
-		*pp = p;
-		return 0;
-
-	}
-
-	return 1;
-}
-
-
-static void check_extents(struct panel p, double *min_x, double *min_y,
-                          double *max_x, double *max_y, double fs, double ss)
-{
-	double xs, ys, rx, ry;
-
-	xs = fs*p.fsx + ss*p.ssx;
-	ys = fs*p.fsy + ss*p.ssy;
-
-	rx = xs + p.cnx;
-	ry = ys + p.cny;
-
-	if ( rx > *max_x ) *max_x = rx;
-	if ( ry > *max_y ) *max_y = ry;
-	if ( rx < *min_x ) *min_x = rx;
-	if ( ry < *min_y ) *min_y = ry;
-}
-
-
-static void rewrite_panel_fields(const struct panel *p, char *line,
-                                 FILE *fh, char **bits,
-                                 int write_panel_coffset)
-{
-	char new_line[1024];
-	char string_to_write[512];
-
-	strcpy(new_line,"\0");
-	strcpy(string_to_write,"\0");
-
-	if(strstr(bits[1], "fs") != NULL &&
-	   strstr(bits[1], "min_fs") == NULL &&
-	   strstr(bits[1], "max_fs") == NULL &&
-	   strstr(bits[1], "offset") == NULL   ) {
-
-		sprintf(string_to_write, "%+fx %+fy",
-			p->fsx, p->fsy);
-		build_output_line(line, new_line,
-		                  string_to_write);
-		fputs(new_line, fh);
-		fputs("\n", fh);
-		return;
-
-	} else if ( strstr(bits[1], "ss") != NULL &&
-		    strstr(bits[1], "min_ss") == NULL &&
-		    strstr(bits[1], "max_ss") == NULL) {
-
-		sprintf(string_to_write, "%+fx %+fy",
-			p->ssx, p->ssy);
-		build_output_line(line, new_line,
-		                  string_to_write);
-		fputs(new_line, fh);
-		fputs("\n", fh);
-		return;
-
-	} else if ( strstr(bits[1], "corner_x") != NULL) {
-
-		sprintf(string_to_write, "%g",
-			p->cnx);
-		build_output_line(line, new_line,
-		                  string_to_write);
-		fputs(new_line, fh);
-		fputs("\n", fh);
-		return;
-
-	} else if ( strstr(bits[1], "corner_y") != NULL) {
-
-		sprintf(string_to_write, "%g",
-			p->cny);
-		build_output_line(line, new_line,
-		                  string_to_write);
-		fputs(new_line, fh);
-		fputs("\n", fh);
-		return;
-
-	} else if ( strstr(bits[1], "coffset") != NULL) {
-
-		if ( write_panel_coffset ) {
-			return;
-		} else {
-			fputs(line, fh);
-		fputs("\n", fh);
-			return;
-		}
-
-	} else {
-		fputs(line, fh);
-		fputs("\n", fh);
-	}
-}
-
-
-double largest_q(struct image *image)
-{
-	struct rvec q;
-	double tt;
-
-	if ( image->det == NULL ) {
-		ERROR("No detector geometry. assuming detector is infinite!\n");
-		return INFINITY;
-	}
-
-	q = get_q_for_panel(image->det->furthest_out_panel,
-	                    image->det->furthest_out_fs,
-	                    image->det->furthest_out_ss,
-	                    &tt, 1.0/image->lambda);
-
-	return modulus(q.u, q.v, q.w);
-}
-
-
-double smallest_q(struct image *image)
-{
-	struct rvec q;
-	double tt;
-
-	q = get_q_for_panel(image->det->furthest_in_panel,
-	                    image->det->furthest_in_fs,
-	                    image->det->furthest_in_ss,
-	                    &tt, 1.0/image->lambda);
-
-	return modulus(q.u, q.v, q.w);
-}
-
-
-void get_pixel_extents(struct detector *det,
-                       double *min_x, double *min_y,
-                       double *max_x, double *max_y)
-{
-	int i;
-
-	*min_x = 0.0;
-	*max_x = 0.0;
-	*min_y = 0.0;
-	*max_y = 0.0;
-
-	/* To determine the maximum extents of the detector, put all four
-	 * corners of each panel through the transformations and watch for the
-	 * biggest */
-
-	for ( i=0; i<det->n_panels; i++ ) {
-
-		check_extents(det->panels[i], min_x, min_y, max_x, max_y,
-		              0.0, 0.0);
-
-		check_extents(det->panels[i], min_x, min_y, max_x, max_y,
-		              0.0, det->panels[i].h+1);
-
-		check_extents(det->panels[i], min_x, min_y, max_x, max_y,
-		              det->panels[i].w+1, 0.0);
-
-		check_extents(det->panels[i], min_x, min_y, max_x, max_y,
-		              det->panels[i].w+1, det->panels[i].h+1);
-
-
-	}
-}
-
-
-int write_detector_geometry_3(const char *geometry_data,
-                              const char *output_filename, struct detector *det,
-                              const char *additional_comment,
-                              int write_panel_coffset)
-{
-	FILE *fh;
-	int done = 0;
-
-	if ( geometry_data == NULL ) return 2;
-	if ( output_filename == NULL ) return 2;
-	if ( det->n_panels < 1 ) return 3;
-
-	fh = fopen(output_filename, "w");
-	if ( fh == NULL ) return 1;
-
-	if ( additional_comment != NULL ) {
-		fputs("; ", fh);
-		fputs(additional_comment, fh);
-		fputs("\n", fh);
-	}
-
-	if  ( write_panel_coffset ) {
-		fputs("; Optimized panel offsets can be found at the "
-		      "end of the file\n", fh);
-	}
-
-	do {
-
-		int n_bits;
-		char **bits;
-		int i;
-		struct panel *p;
-		char *line;
-		const char *nl;
-
-		/* Get the next line */
-		nl = strchr(geometry_data, '\n');
-		if ( nl != NULL ) {
-			size_t len = nl - geometry_data;
-			line = strndup(geometry_data, nl-geometry_data);
-			line[len] = '\0';
-			geometry_data += len+1;
-		} else {
-			/* Last line might now have newline at end */
-			line = strdup(geometry_data);
-			done = 1;
-		}
-
-		n_bits = assplode(line, "/=", &bits, ASSPLODE_NONE);
-
-		if ( n_bits != 3 ) {
-			if ( write_panel_coffset && (bits != NULL)
-			    && (strstr(bits[0], "coffset" ) != NULL) ) continue;
-			fputs(line, fh);
-			fputs("\n", fh);
-		} else {
-
-			p = find_panel_by_name(det, bits[0]);
-
-			if ( p != NULL ) {
-				rewrite_panel_fields(p, line, fh, bits,
-						     write_panel_coffset);
-			} else {
-				fputs(line, fh);
-				fputs("\n", fh);
-			}
-		}
-
-		for ( i=0; i<n_bits; i++ ) free(bits[i]);
-
-	} while ( !done );
-
-	if ( write_panel_coffset ) {
-
-		int pi;
-
-		fputs("\n", fh);
-
-		for ( pi=0; pi<det->n_panels; pi++ ) {
-			fprintf(fh, "%s/coffset = %f\n",
-			        det->panels[pi].name, det->panels[pi].coffset);
-		}
-	}
-
-	return 0;
-}
-
-
-int write_detector_geometry_2(const char *geometry_filename,
-                              const char *output_filename, struct detector *det,
-                              const char *additional_comment,
-                              int write_panel_coffset)
-{
-	int r;
-	char *geometry_data = load_entire_file(geometry_filename);
-	r = write_detector_geometry_3(geometry_data, output_filename, det,
-	                              additional_comment, write_panel_coffset);
-	free(geometry_data);
-	return r;
-}
-
-
-int write_detector_geometry(const char *geometry_filename,
-                            const char *output_filename, struct detector *det)
-{
-	return write_detector_geometry_2(geometry_filename, output_filename,
-	                                 det, NULL, 0);
-}
-
-
-/**
- * \param image An image structure
- * \param min Minimum value of 1/d to be marked as bad
- * \param max Maximum value of 1/d to be marked as bad
- *
- * Flags, in the bad pixel mask for \p image, every pixel whose resolution is
- * between \p min and \p max.
- *
- */
-
-void mark_resolution_range_as_bad(struct image *image,
-                                  double min, double max)
-{
-	int i;
-
-	if ( isinf(min) && isinf(max) ) return;  /* nothing to do */
-
-	for ( i=0; i<image->det->n_panels; i++ ) {
-
-		int fs, ss;
-		struct panel *p = &image->det->panels[i];
-
-		for ( ss=0; ss<p->h; ss++ ) {
-		for ( fs=0; fs<p->w; fs++ ) {
-			struct rvec q;
-			double r;
-			q = get_q_for_panel(p, fs, ss, NULL, 1.0/image->lambda);
-			r = modulus(q.u, q.v, q.w);
-			if ( (r >= min) && (r <= max) ) {
-				image->bad[i][fs+p->w*ss] = 1;
-			}
-		}
-		}
-
-	}
-}
-
-
-static int safe_strcmp(const char *a, const char *b)
-{
-	/* If both are NULL, they count as equal */
-	if ( (a == NULL) && (b == NULL) ) return 0;
-
-	/* Otherwise, if either is NULL then they're different */
-	if ( a == NULL ) return 1;
-	if ( b == NULL ) return 1;
-
-	/* Otherwise, normal string comparison */
-	return strcmp(a, b);
-}
-
-
-/**
- * \param det A detector structure
- * \param element If manually selected by the user, the HDF5 element being used.
- * Otherwise NULL.
- *
- * \returns Non-zero if the combination of \p det and \p element mean that all the
- * data comes from a single block.
- */
-int single_panel_data_source(struct detector *det, const char *element)
-{
-	int pi;
-	const char *first_datafrom = NULL;
-	const char *curr_datafrom = NULL;
-
-	if ( det->panels[0].data == NULL ) {
-		first_datafrom = element; /* Might be NULL */
-	} else {
-		first_datafrom = det->panels[0].data;
-	}
-
-	for ( pi=1; pi<det->n_panels; pi++ ) {
-
-		if ( det->panels[pi].data == NULL ) {
-			curr_datafrom = element; /* Might be NULL */
-		} else {
-			curr_datafrom = det->panels[pi].data;
-		}
-
-		if ( safe_strcmp(curr_datafrom, first_datafrom) != 0 ) {
-			return 0;
-		}
-
-	}
-
-	return 1;
-}
-
-
-int multi_event_geometry(struct detector *det)
-{
-	return (det->path_dim != 0) || (det->dim_dim != 0);
-}
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
deleted file mode 100644
index 2176861f..00000000
--- a/libcrystfel/src/detector.h
+++ /dev/null
@@ -1,333 +0,0 @@
-/*
- * detector.h
- *
- * Detector properties
- *
- * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
- *                       a research centre of the Helmholtz Association.
- * Copyright © 2012 Richard Kirian
- *
- * Authors:
- *   2009-2019 Thomas White <taw@physics.org>
- *   2011-2012 Richard Kirian <rkirian@asu.edu>
- *   2014      Valerio Mariani
- *   2011      Andrew Aquila
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#ifndef DETECTOR_H
-#define DETECTOR_H
-
-struct rigid_group;
-struct rg_collection;
-struct detector;
-struct panel;
-struct badregion;
-struct beam_params;
-struct hdfile;
-struct event;
-
-#include "hdf5-file.h"
-#include "image.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/**
- * \file detector.h
- * Detector geometry structure and related functions.
- */
-
-
-struct rigid_group
-{
-	char *name;
-	struct panel **panels;
-	int n_panels;
-};
-
-
-struct rg_collection
-{
-	char *name;
-	struct rigid_group **rigid_groups;
-	int n_rigid_groups;
-};
-
-
-/**
- * Represents one panel of a detector
- */
-struct panel
-{
-	/** Text name for panel (fixed length array) */
-	char     name[1024];
-
-	/** \name Location of corner in units of the pixel size of this panel */
-	/**@{*/
-	double   cnx;
-	double   cny;
-	/**@}*/
-
-	/** The offset to be applied from \ref clen */
-	double   coffset;
-
-	/** The distance from the interaction point to the corner of the
-	 * first pixel */
-	double   clen;
-
-	/** Location to get \ref clen from, e.g. from HDF5 file */
-	char    *clen_from;
-
-	/** Location of mask data */
-	char    *mask;
-
-	/** Filename for mask data */
-	char    *mask_file;
-
-	/** Location of per-pixel saturation map */
-	char    *satmap;
-
-	/** Filename for saturation map */
-	char    *satmap_file;
-
-	/** Resolution in pixels per metre  */
-	double   res;
-
-	/** Readout direction (for filtering out clusters of peaks)
-	  * ('x' or 'y') */
-	char     badrow;
-
-	/** Non-zero if panel should be considered entirely bad */
-	int      no_index;
-
-	/** Number of detector intensity units per photon */
-	double   adu_per_photon;
-
-	/** Treat pixel as unreliable if higher than this */
-	double   max_adu;
-
-	/** Location of data in file */
-	char    *data;
-
-	/** Number of detector intensity units per eV of photon energy */
-	double   adu_per_eV;
-
-	/** Dimension structure */
-	struct dim_structure *dim_structure;
-
-	/** \name Transformation matrix from pixel coordinates to lab frame */
-	/*@{*/
-	double fsx;
-	double fsy;
-	double fsz;
-	double ssx;
-	double ssy;
-	double ssz;
-	/*@}*/
-
-	/** \name Rail direction */
-	/*@{*/
-	double rail_x;
-	double rail_y;
-	double rail_z;
-	/*@}*/
-
-	/* Value of clen (without coffset) at which beam is centered */
-	double clen_for_centering;
-
-	/** \name Inverse of 2D part of transformation matrix */
-	/*@{*/
-	double xfs;
-	double yfs;
-	double xss;
-	double yss;
-	/*@}*/
-
-	/** \name Position of the panel in the data block in the file.
-	 * The panels may get moved around when the file is loaded (see
-	 * hdf5_read2()), especially if the panels come from different HDF5
-	 * elements. */
-	/*@{*/
-	int orig_min_fs;
-	int orig_max_fs;
-	int orig_min_ss;
-	int orig_max_ss;
-	/*@}*/
-
-	/** Width, calculated as max_fs-min_fs+1 */
-	int w;
-
-	/*** Height, calculated as max_ss-min_ss+1 */
-	int h;
-};
-
-
-struct badregion
-{
-	char name[1024];
-	int is_fsss;
-	char *panel;
-
-	double min_x;
-	double max_x;
-	double min_y;
-	double max_y;
-
-	/* Specified INCLUSIVELY */
-	int      min_fs;
-	int      max_fs;
-	int      min_ss;
-	int      max_ss;
-
-};
-
-
-struct detector
-{
-	struct panel     *panels;
-	int               n_panels;
-
-	struct badregion *bad;
-	int               n_bad;
-
-	unsigned int      mask_bad;
-	unsigned int      mask_good;
-
-	struct rigid_group **rigid_groups;
-	int                  n_rigid_groups;
-
-	struct rg_collection **rigid_group_collections;
-	int                    n_rg_collections;
-
-	/* Location of the pixel furthest away from the beam position, which
-	 * will have the largest value of 2theta regardless of camera length
-	 * and wavelength */
-	struct panel      *furthest_out_panel;
-	double             furthest_out_fs;
-	double             furthest_out_ss;
-
-	/* As above, but for the smallest 2theta */
-	struct panel      *furthest_in_panel;
-	double             furthest_in_fs;
-	double             furthest_in_ss;
-
-	int                path_dim;
-	int                dim_dim;
-
-	struct panel       defaults;
-};
-
-
-extern struct rvec get_q_for_panel(struct panel *p, double fs, double ss,
-                                   double *ttp, double k);
-
-extern double get_tt(struct image *image, double xs, double ys, int *err);
-
-extern int in_bad_region(struct detector *det, struct panel *p,
-                         double fs, double ss);
-
-extern void record_image(struct image *image, int do_poisson, double background,
-                         gsl_rng *rng, double beam_radius, double nphotons);
-
-extern struct panel *find_orig_panel(struct detector *det,
-                                     double fs, double ss);
-
-extern signed int find_orig_panel_number(struct detector *det,
-                                         double fs, double ss);
-
-extern int panel_number(const struct detector *det, const struct panel *p);
-
-extern struct detector *get_detector_geometry(const char *filename,
-                                              struct beam_params *beam);
-
-extern struct detector *get_detector_geometry_2(const char *filename,
-                                                struct beam_params *beam,
-                                                char **hdf5_peak_path);
-
-extern struct detector *get_detector_geometry_from_string(const char *string,
-                                                          struct beam_params *beam,
-                                                          char **hdf5_peak_path);
-
-extern void free_detector_geometry(struct detector *det);
-
-extern struct detector *simple_geometry(const struct image *image, int w, int h);
-
-extern void get_pixel_extents(struct detector *det,
-                              double *min_x, double *min_y,
-                              double *max_x, double *max_y);
-
-extern void fill_in_adu(struct image *image);
-extern void adjust_centering_for_rail(struct panel *p);
-
-extern int panel_is_in_rigid_group(const struct rigid_group *rg,
-                                   struct panel *p);
-
-extern int rigid_group_is_in_collection(struct rg_collection *c,
-                                        struct rigid_group *rg);
-
-extern struct detector *copy_geom(const struct detector *in);
-
-extern int reverse_2d_mapping(double x, double y, struct detector *det,
-                              struct panel **pp, double *pfs, double *pss);
-
-extern double largest_q(struct image *image);
-
-extern double smallest_q(struct image *image);
-
-extern struct panel *find_panel_by_name(struct detector *det, const char *name);
-
-extern int write_detector_geometry_2(const char *geometry_filename,
-                                     const char *output_filename,
-                                     struct detector *det,
-                                     const char *additional_comment,
-                                     int write_panel_coffset);
-
-extern int write_detector_geometry_3(const char *geometry_data,
-                                     const char *output_filename,
-                                     struct detector *det,
-                                     const char *additional_comment,
-                                     int write_panel_coffset);
-
-extern int write_detector_geometry(const char *geometry_filename,
-                                   const char *output_filename,
-                                   struct detector *det);
-
-extern void mark_resolution_range_as_bad(struct image *image,
-                                         double min, double max);
-
-
-extern int single_panel_data_source(struct detector *det, const char *element);
-
-struct rg_collection *find_rigid_group_collection_by_name(struct detector *det,
-                                                          const char *name);
-
-extern int detector_has_clen_references(struct detector *det);
-
-extern int multi_event_geometry(struct detector *det);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif	/* DETECTOR_H */
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 44ce24ac..0235e0c2 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -35,19 +35,15 @@
 #ifndef IMAGE_H
 #define IMAGE_H
 
-struct detector;
-
 #include <stdint.h>
 #include <complex.h>
 #include <sys/types.h>
 
 struct imagefeature;
-struct sample;
 struct image;
 
 #include "utils.h"
 #include "cell.h"
-#include "detector.h"
 #include "reflist.h"
 #include "crystal.h"
 #include "index.h"
@@ -101,17 +97,6 @@ enum imagefile_type
 typedef struct _imagefeaturelist ImageFeatureList;
 
 
-struct beam_params
-{
-	double photon_energy;       /**< eV per photon */
-	char  *photon_energy_from;  /**< HDF5 dataset name */
-	double photon_energy_scale; /**< Scale factor for photon energy, if it
-	                             *   comes from an image header */
-	double bandwidth;           /**< FWHM bandwidth as a fraction of
-	                             *   wavelength */
-};
-
-
 struct image
 {
 	/** The image data, by panel */
@@ -138,14 +123,8 @@ struct image
 	/** Number of times the indexer was tried before succeeding */
 	int                     n_indexing_tries;
 
-	/** The detector structure
-	 * @{ */
+	/** The detector structure */
 	struct detgeom          *detgeom;
-	struct detector         *det;   /* FIXME: Deprecated */
-	/** @} */
-
-	/** The nominal beam parameters (or where to get them) */
-	struct beam_params      *beam;  /* FIXME: Deprecated */
 
 	/** \name The filename and event ID for the image
 	 * @{ */
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 1fce0f60..9a144a36 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -116,6 +116,132 @@ static void show_help(const char *s)
 }
 
 
+static void record_panel(struct panel *p, float *dp, int do_poisson,
+                         gsl_rng *rng, double ph_per_e, double background,
+			 double lambda,
+                         int *n_neg1, int *n_inf1, int *n_nan1,
+                         int *n_neg2, int *n_inf2, int *n_nan2,
+			 double *max_tt)
+{
+	int fs, ss;
+
+	for ( ss=0; ss<p->h; ss++ ) {
+	for ( fs=0; fs<p->w; fs++ ) {
+
+		double counts;
+		double cf;
+		double intensity, sa;
+		double pix_area, Lsq;
+		double xs, ys, rx, ry;
+		double dsq, proj_area;
+		float dval;
+		double twotheta;
+
+		intensity = (double)dp[fs + p->w*ss];
+		if ( isinf(intensity) ) (*n_inf1)++;
+		if ( intensity < 0.0 ) (*n_neg1)++;
+		if ( isnan(intensity) ) (*n_nan1)++;
+
+		/* Area of one pixel */
+		pix_area = pow(1.0/p->res, 2.0);
+		Lsq = pow(p->clen, 2.0);
+
+		/* Calculate distance from crystal to pixel */
+		xs = fs*p->fsx + ss*p->ssx;
+		ys = ss*p->fsy + ss*p->ssy;
+		rx = (xs + p->cnx) / p->res;
+		ry = (ys + p->cny) / p->res;
+		dsq = pow(rx, 2.0) + pow(ry, 2.0);
+		twotheta = atan2(sqrt(dsq), p->clen);
+
+		/* Area of pixel as seen from crystal (approximate) */
+		proj_area = pix_area * cos(twotheta);
+
+		/* Projected area of pixel divided by distance squared */
+		sa = proj_area / (dsq + Lsq);
+
+		if ( do_poisson ) {
+			counts = poisson_noise(rng, intensity * ph_per_e * sa);
+		} else {
+			cf = intensity * ph_per_e * sa;
+			counts = cf;
+		}
+
+		/* Number of photons in pixel */
+		dval = counts + poisson_noise(rng, background);
+
+		/* Convert to ADU */
+		dval *= p->adu_per_photon;
+
+		/* Saturation */
+		if ( dval > p->max_adu ) dval = p->max_adu;
+
+		dp[fs + p->w*ss] = dval;
+
+		/* Sanity checks */
+		if ( isinf(dp[fs + p->w*ss]) ) n_inf2++;
+		if ( isnan(dp[fs + p->w*ss]) ) n_nan2++;
+		if ( dp[fs + p->w*ss] < 0.0 ) n_neg2++;
+
+		if ( twotheta > *max_tt ) *max_tt = twotheta;
+
+	}
+	}
+}
+
+
+void record_image(struct image *image, int do_poisson, double background,
+                  gsl_rng *rng, double beam_radius, double nphotons)
+{
+	double total_energy, energy_density;
+	double ph_per_e;
+	double area;
+	double max_tt = 0.0;
+	int n_inf1 = 0;
+	int n_neg1 = 0;
+	int n_nan1 = 0;
+	int n_inf2 = 0;
+	int n_neg2 = 0;
+	int n_nan2 = 0;
+	int pn;
+
+	/* How many photons are scattered per electron? */
+	area = M_PI*pow(beam_radius, 2.0);
+	total_energy = nphotons * ph_lambda_to_en(image->lambda);
+	energy_density = total_energy / area;
+	ph_per_e = (nphotons /area) * pow(THOMSON_LENGTH, 2.0);
+	STATUS("Fluence = %8.2e photons, "
+	       "Energy density = %5.3f kJ/cm^2, "
+	       "Total energy = %5.3f microJ\n",
+	       nphotons, energy_density/1e7, total_energy*1e6);
+
+	fill_in_adu(image);
+
+	for ( pn=0; pn<image->det->n_panels; pn++ ) {
+
+		record_panel(&image->det->panels[pn], image->dp[pn],
+		             do_poisson, rng, ph_per_e, background,
+			     image->lambda,
+		             &n_neg1, &n_inf1, &n_nan1,
+		             &n_neg2, &n_inf2, &n_nan2, &max_tt);
+	}
+
+	STATUS("Max 2theta = %.2f deg, min d = %.2f nm\n",
+	        rad2deg(max_tt), (image->lambda/(2.0*sin(max_tt/2.0)))/1e-9);
+
+	STATUS("Halve the d values to get the voxel size for a synthesis.\n");
+
+	if ( n_neg1 + n_inf1 + n_nan1 + n_neg2 + n_inf2 + n_nan2 ) {
+		ERROR("WARNING: The raw calculation produced %i negative"
+		      " values, %i infinities and %i NaNs.\n",
+		      n_neg1, n_inf1, n_nan1);
+		ERROR("WARNING: After processing, there were %i negative"
+		      " values, %i infinities and %i NaNs.\n",
+		      n_neg2, n_inf2, n_nan2);
+	}
+}
+
+
 static double *intensities_from_list(RefList *list, SymOpList *sym)
 {
 	Reflection *refl;